Hi there,
I am currently running simulations of a protein-DNA complex. As my complex is quite huge, I am running 10 ns step by step.
Due to this, I have a new tpr file for each 10 ns.
When I want to add all of the output trajectory (xtc) files in the end, I am now wondering which tpr file to use for the trjconv command? the first input file or rather the latest? And can I use different one (more uptodate) if I want to add later on again some ns-trajectory? Also, when I am centering the complex or want to delete some frames for better handling of the huge files, I need a tpr file and do not know which one to use in each case?
Would be great if someone could help me :)
the commands I am currently using are the following:
gmx trjconv -f md_0.8.gro -s md_0.8_2.tpr -pbc mol -center -ur compact -o centered.gro
gmx trjcat -f md_10.xtc md_20.part0002.xtc -o final.xtc
gmx trjconv -f final_20ns_0.8.xtc -s md_0.8_2.tpr -dt 1000 -o system_lessframes.xtc
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center
gmx trjcat -f md_10.xtc md_20.part0002.xtc -o final.xtc